90297a90d259da8b7e7d48e7bf8600994e6a09a6
hiram
  Wed Jun 10 07:23:05 2026 -0700
minor fixups per claude code review refs #31811

diff --git src/hg/utils/otto/userRequests/asmRequestWatch.sh src/hg/utils/otto/userRequests/asmRequestWatch.sh
index c2635866144..ee738571595 100755
--- src/hg/utils/otto/userRequests/asmRequestWatch.sh
+++ src/hg/utils/otto/userRequests/asmRequestWatch.sh
@@ -1,18 +1,18 @@
 #!/bin/bash
 
-# asmRequestWatch.sh - what for assembly requests in the ottoRequest table
+# asmRequestWatch.sh - watch for assembly requests in the ottoRequest table
 #
 # Initial function is just to watch the status, and when it
 #   reaches status 6 'push complete' (which currently is set manually)
 #   then send email and mark finished
 #
 # The 'otto' user cron job 'ottoRequest.py' will be watching for status 0
 #   for a new entry.  It will set status 1 and send notification email
 #
 # Different meanings from the liftOver status settings:
 #   0 pending, 1 notified, 2 in progress, 6 push is done and is available on the RR,
 #      status 7 for problems, and 8 is final notification has been sent == process is complete
 ### cron job entry: (1 minute later than ottoRequestWatch.sh)
 # 10,21,32,43,54 * * * * ~/kent/src/hg/utils/otto/userRequests/asmRequestWatch.sh
 
 set -eEu -o pipefail
@@ -37,40 +37,39 @@
 # 9<> opens read+write without truncating, so a second instance that
 # comes along while we're running won't wipe our PID from the file
 # before its flock attempt fails.
 exec 9<>"${lockPath}"
 flock -n 9 || exit 0
 # we own the lock now safe to truncate and write our PID.  ': >file'
 # truncates via a separate FD; FD 9 keeps its position 0 from <>, so
 # the printf below starts writing at the beginning of the empty file.
 : >"${lockPath}"
 printf "%d\n" "$$" >&9
 ##############################################################################
 
 ##############################################################################
 ### errors - set error status in the table
 function setErrorStatus() {
-  id="${1}"
+  local id="${1}"
   /cluster/bin/x86_64/${hgSql} -N -e \
       "UPDATE ottoRequest SET status=7 WHERE id=${id};" "${centDb}"
 }
 ##############################################################################
 
 ##############################################################################
 ### sendNotification - email the requesting user that their assembly request is done
-###   args: reqId subject
-###   message body is read from stdin
+###   args: reqId subject msgBody
 ###   recipient: email column of ottoRequest table for that reqId
 ###   bcc: genark-request-group@ucsc.edu
 ###   envelope sender / Return-Path / bounce: genome-www@soe.ucsc.edu
 ###   returns 0 on success, non-zero on failure
 ##############################################################################
 function sendNotification() {
   local reqId="${1}"
   local subject="${2}"
   local msgBody="${3}"
   local toAddr
   toAddr="$(/cluster/bin/x86_64/${hgSql} -N -B -e \
     "SELECT email FROM ottoRequest WHERE id = ${reqId};" ${centDb})"
   if [ -z "${toAddr}" ]; then
     printf "ERROR: sendNotification: no email for request %s\n" "${reqId}" 1>&2
     return 1
@@ -277,36 +276,36 @@
       setErrorStatus "${reqId}"
       ;;
   esac
 
 done < <(/cluster/bin/x86_64/${hgSql} -N -B -e \
   "SELECT id, fromDb FROM ottoRequest WHERE status = 5 AND requestType = 'assembly';" \
   ${centDb})
 
 ############################################################################
 # check for phase 6: the assembly is complete and available on the RR
 #       this checking and setting status 6 is currently done manually,
 #       eventually this will become automatic.
 ############################################################################
 while IFS=$'\t' read -r reqId fromDb comment requestTime; do
 
-  export gcX="${fromDb:0:3}"
-  export d0="${fromDb:4:3}"
-  export d1="${fromDb:7:3}"
-  export d2="${fromDb:10:3}"
-  export gbDbPath="/gbdb/genark/${gcX}/${d0}/${d1}/${d2}/${fromDb}/hub.txt"
-  export hubTxt="https://genome.ucsc.edu/cgi-bin/hgTracks?genome=${fromDb}&hubUrl=${gbDbPath}"
+  gcX="${fromDb:0:3}"
+  d0="${fromDb:4:3}"
+  d1="${fromDb:7:3}"
+  d2="${fromDb:10:3}"
+  gbDbPath="/gbdb/genark/${gcX}/${d0}/${d1}/${d2}/${fromDb}/hub.txt"
+  hubTxt="https://genome.ucsc.edu/cgi-bin/hgTracks?genome=${fromDb}&hubUrl=${gbDbPath}"
 
   sendNotification "${reqId}" \
 "from UCSC: assembly request complete: ${fromDb}" \
 "from UCSC: Your assembly request is complete:
  assembly:     ${fromDb}
   comment:     ${comment}
 submitted:     ${requestTime}
 
 The assembly is available in the browser at the following URL:
   ${hubTxt}
 "
 
 /cluster/bin/x86_64/${hgSql} -N -e \
       "UPDATE ottoRequest SET status=8, completeTime=now() WHERE id=${reqId};" ${centDb}